mmseqs2 expandaln receives an unrecognised parameter --db-load-mode in search.py

[dingquanyu]

Hi,

I've freshly installed mmseqs2 and colabfold then running colab_search.py gave me the error:

subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'expandaln', PosixPath('msas/qdb'), PosixPath('/scratch/gchojnowski/dbs/uniref30_2103_db.idx'), PosixPath('msas/res'), PosixPath('/scratch/gchojnowski/dbs/uniref30_2103_db.idx'), PosixPath('msas/res_exp'), '--db-load-mode', '0', '--threads', '64', '--expansion-mode', '0', '-e', 'inf', '--expand-filter-clusters', '1', '--max-seq-id', '0.95']' returned non-zero exit status 1.

This is owning to the db-load-mode in this line:https://github.com/sokrypton/ColabFold/blob/22671664ac2c9dcb30086c3e654414d950ccb297/colabfold/mmseqs/search.py#L108 I don't think in this line within the search.py, db-load-mode is supposed to be there? I've checked that mmseqs expandaln doesn't take db-load-mode as a parameter.

Yours Dingquan

[real-junjiezhang]

hi may i ask whether you resolve this issue? thanks, i met the same problem.

[milot-mirdita]

This should only happen if you use a very old MMseqs2 issue with colabfold_search. Please update MMseqs2